There is no way that Rose Tyler can be called a Mary Sue by any definition of the term. It gets thrown around a lot as a sort of blanket expression for characters that people don't like, regardless of whether it actually applies. From a certain perspective you could say that she did get put on a bit of a pedestal after a while, but the only 'criticism' anyone could reasonably make of her character is that she was young and in love with someone she didn't completely understand. I can't find it in my heart to condemn her for that, and I really don't understand those who do.

River Song is so smugly irritating and convinced of her own importance that at this point I don't care who the hell she is--I just wish she would cease to exist.

I'll easily acknowledge that Amy is the most physically attractive companion they've had on the show, but unfortunately her personality is shallow and abrasively nonexistant. If there are women like her in real life, that only goes to show that it isn't only fictional characters who lack depth.